Hi,
Sorry for the duplicate, I think my answer to the previous thread I started didn't get through.
I am trying to parametrize a non-standard residue (biliverdin) covalently bound to a cysteine residue. I am following the Amber tutorial: Simulating the Green Fluorescent Protein and Building a Modified Amino Acid Residue. I downloaded the .ciff file for the JRA ligand from PDB, produced the .ac file using antechamber, and my .mc file looks like this:
HEAD_NAME CAC
TAIL_NAME CAC
OMIT_NAME H27
PRE_HEAD_TYPE SG
POST_TAIL_TYPE SG
CHARGE 0.0
where CAC is the atomname of the biliverdin atom that is covalently bound to the SG atom of the nearby cysteine residue (which I renamed as CYX instead of CYS), and H27 is the hydrogen that I need to omit from the ligand to create the bond.
After creating the .frmod and prepin files for my ligand from the tutorial, I get to the tleap step. My tleap input file looks like this:
source leaprc.protein.ff19SB
loadAmberPrep JRA.prepin
loadAmberParams frcmod2.cro
loadAmberParams frcmod1.cro
x = loadPDB miRFP670nano_BV_h1.pdb
#bond x.86.SG x.148.CAC
saveAmberParm x miRFP670nano_BV.parm7 miRFP670nano_BV.rst7
quit
When the "bond" line is commented, tleap doesn't give errors, but the parm7 an rst7 files do not have the bond between SG and CAC. If I include the bond line, tleap produces this error message:
/proj/pierilab/software/amber/cuda12.2_version/amber22/bin/teLeap: Error!
Could not find bond parameter for atom types: S - CM
for atom SG at position 42.321000, -4.195000, 17.484000
and atom CAC at position 42.271000, -5.667000, 18.332000.
Building angle parameters.
/proj/pierilab/software/amber/cuda12.2_version/amber22/bin/teLeap: Error!
Could not find angle parameter for atom types: S - CM - CM
for atom SG at position 42.321000, -4.195000, 17.484000,
atom CAC at position 42.271000, -5.667000, 18.332000,
and atom CBC at position 42.998000, -6.719000, 17.994000.
/proj/pierilab/software/amber/cuda12.2_version/amber22/bin/teLeap: Error!
Could not find angle parameter for atom types: S - CM - CT
for atom SG at position 42.321000, -4.195000, 17.484000,
atom CAC at position 42.271000, -5.667000, 18.332000,
and atom C3C at position 41.383000, -5.509000, 19.575000.
/proj/pierilab/software/amber/cuda12.2_version/amber22/bin/teLeap: Error!
Could not find angle parameter for atom types: 2C - S - CM
for atom CB at position 40.786000, -3.743000, 16.703000,
atom SG at position 42.321000, -4.195000, 17.484000,
and atom CAC at position 42.271000, -5.667000, 18.332000.
Building proper torsion parameters.
/proj/pierilab/software/amber/cuda12.2_version/amber22/bin/teLeap: Error!
** No torsion terms for atom types: 2C-S-CM-CM
for atom CB at position 40.786000, -3.743000, 16.703000,
atom SG at position 42.321000, -4.195000, 17.484000,
atom CAC at position 42.271000, -5.667000, 18.332000,
and atom CBC at position 42.998000, -6.719000, 17.994000.
/proj/pierilab/software/amber/cuda12.2_version/amber22/bin/teLeap: Error!
** No torsion terms for atom types: 2C-S-CM-CT
for atom CB at position 40.786000, -3.743000, 16.703000,
atom SG at position 42.321000, -4.195000, 17.484000,
atom CAC at position 42.271000, -5.667000, 18.332000,
and atom C3C at position 41.383000, -5.509000, 19.575000.
Building improper torsion parameters.
old PREP-specified impropers:
<JRA 148>: CBC C3C CAC -M
<JRA 148>: CAC H28 CBC H29
<JRA 148>: C2C NC C1C OC
<JRA 148>: C1C C4C NC H20
<JRA 148>: CHD C3C C4C NC
<JRA 148>: C1D C4C CHD H30
<JRA 148>: C2D CHD C1D ND
<JRA 148>: C3D CHA C4D ND
<JRA 148>: C4D C1A CHA H1
<JRA 148>: C2A CHA C1A NA
<JRA 148>: C1A C4A NA H3
<JRA 148>: C3A CHB C4A NA
<JRA 148>: C2A C4A C3A CMA
<JRA 148>: C3A C1A C2A CAA
<JRA 148>: CBA O1A CGA O2A
<JRA 148>: C4A C1B CHB H12
<JRA 148>: C2B CHB C1B NB
<JRA 148>: C4B C1B NB H2
<JRA 148>: C3B NB C4B OB
<JRA 148>: C2B C4B C3B CAB
<JRA 148>: C3B C1B C2B CMB
<JRA 148>: C3B CBB CAB H17
<JRA 148>: CAB H18 CBB H19
<JRA 148>: C2D C4D C3D CAD
<JRA 148>: C3D C1D C2D CMD
<JRA 148>: CBD O2D CGD O1D
total 526 improper torsions applied
26 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
/proj/pierilab/software/amber/cuda12.2_version/amber22/bin/teLeap: Warning!
Parameter file was not saved.
Quit
Exiting LEaP: Errors = 6; Warnings = 2; Notes = 1.
What am I missing? How do I parametrize this bond correctly? Should I use a different atom type for either the sulfur (instead of SG/SH) or the CAC atom (instead of CM)?
Thank you in advance,
Noureen
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Received on Thu Feb 08 2024 - 10:30:02 PST
